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bartongroup / Simpson_Barton_Nanopore_1

jupyter notebooks for Parker et al. eLife 2019
MIT License
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Blastn parameters #6

Open nemitheasura opened 3 years ago

nemitheasura commented 3 years ago

May I ask you for the exact blastn parameters (adapter filtering pipe) used in the first place?

I could not find them, but will appreciate such a knowledge.

Best, N.

mparker2 commented 3 years ago

Hi @nemitheasura,

here are the blast parameters we used to detect 5' adapters in the cap-capture experiment:

https://github.com/bartongroup/Simpson_Barton_Nanopore_1/blob/1b509454a9e25a8c81be5092f8e525ca00e7b5a5/pipeline/basecalling_pipeline/Snakefile#L180-L183

Is this what you meant? Also if you are trying to find short adapter sequences in raw nanopore reads, another possibility which may be more sensitive is to use profile hmms. There is a package called hammerpede which is designed to do this.

nemitheasura commented 3 years ago

Hi @mparker2 ,

thank you very much for your response. Yes, that was exactly what I wanted to know. Thank you very much for clarification.

Can hammerpede be used on DRS data? I thought it is designed for cDNA. I'll give a try then. I already tried to play with cutadapt and IRanges - something promising, promising.

Thank you. Best, N.

mparker2 commented 3 years ago

I don't see why it can't be used for DRS - its all sequences in the end! Hammerpede just trains the pHMM model. Pychopper itself is designed to deal with cDNA data so I think once you have your model you'd need to write a custom script to apply it in the 5' of the reads. I think I might have experimented with this at some stage - I will have a look!

@bsipos is this info correct?